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Exploring Bioinformatics: Gene and Protein Sequence Analysis and Structure Prediction

This resource delves into the intricate world of bioinformatics, emphasizing the connections between gene sequences, protein structures, and their functions. By leveraging databases such as GenBank and EMBL, users can retrieve vital information on genomic sequences and protein structures. The guide also covers analysis techniques, including sequence alignment, structure prediction, and comparative genomics. Whether you are a student or a researcher, this comprehensive overview enhances understanding of molecular biology through the use of online databases and bioinformatics tools.

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Exploring Bioinformatics: Gene and Protein Sequence Analysis and Structure Prediction

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  1. From Sequence to Structure Sources on Web

  2. 生物資訊內涵 • Gene , Protein • 序列, 結構, 功能 • 比對, 預測, 分類 , 關聯, 註解…

  3. In form of codon, Left-Top-Right T C A G T Phe Ser Tyr Cys T C Leu Ter Ter A Trp G C Leu Pro His Arg T C Gln A G A Ile Thr Asn Ser T C Lys Arg A Met G G Val Ala Asp Gly T C Glu A G 基因碼Genetic Code Codon Three bases in a DNA or RNA sequence which specify a single amino acid. http://www.cmbi.kun.nl/swift/future/aainfo/gencode.html

  4. 生物資訊網路資源 Sequence Retrieve System 歐洲生物資訊研究所 The European Bioimformatics Institute http://www.ebi.ac.uk/ http://microbiology.scu.edu.tw/wong/courses/inform/site05.htm

  5. 生物資訊網路資源 資料庫分類 • 主要序列儲存 • 基因體資料庫 • 蛋白質資料庫 • 結構資料庫 • 分子間作用資料庫 • 突變資料庫 • 文獻資料庫

  6. 生物資訊網路資源 基因資料庫 GDB genome databasehttp://gdbwww.gdb.org/ GenbankNIH genetic sequence http://www.ncbi.nlm.nih.gov/Genbank/ Genomenet http://www.genome.jp/ DNA 資料庫 EMBL nucleic acid database http://www.ebi.ac.uk/embl/index.html NDB nucleic acid database http://ndbserver.rutgers.edu/NDB/ RNA 資料庫 RDPrRNA sequences http://rdp.cme.msu.edu/html/

  7. 生物資訊網路資源 蛋白質資料庫 PIR protein Information resources http://pir.georgetown.edu Swiss-Prot/TrEMBL curated protein sequence http://www.expasy.ch/sprot/ PDB protein data bank http://www.rcsb.org/pdb/ CATH protein structure classification http://www.biochem.ucl.ac.uk/bsm/cath_new/ SCOP proteinStructural classification http://scop.mrc-lmb.cam.ac.uk/scop/

  8. 生物資訊網路資源 教學資源 NEE-HOW, POST, 莊榮輝教授教學網業(臺大農化) • 核酸 DNA from the beginning - Cold Spring Harbor Laboratory, New York (USA) Structure of DNA - http://www.umass.edu/molvis/freichsman/NucAcids/Helix/hmenu.html • 胺基酸 Amino acid properties - University of California. Davis (USA) Amino acid information - European Molecular Biology Lab-Heidelberg (German) 蛇毒傳奇-清華大學 (Taiwan) • 蛋白質 Principles of Protein Structure Using the Iternet - Birkbeck College-London (UK) 生物資訊 Using Internet Resources in Molecular Biology-San Diego Supercomputer center(USA) 生命科學線上教學- 清華大學生物資訊中心 (Taiwan) BioInfoFab - 陽明大學生物資訊中心 (Taiwan)

  9. 生物資訊網路資源 參考查詢資源 • HINT - 國家衛生研究院醫藥衛生研究資訊網 (Taiwan) http://www.hint.org.tw/ • Entrez(PubMed)–National Center of biotechnology Information (USA) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

  10. Streptomyces avermitilis is an industrial microorganism produced anthelmintic macrolide Avermectins. http://avermitilis.ls.kitasato-u.ac.jp/

  11. 序列分析與結構預測

  12. 核酸  蛋白質 核酸序列  蛋白質序列  蛋白質性質  蛋白質結構

  13. 基因比對 資料庫:GenBank 工具:Blast

  14. 基因轉譯 核酸序列 網站: Expasy 工具:MBS translator 蛋白質序列

  15. 蛋白質特性pI 質與分子量 網站: Expasy 工具:PI/MW compute

  16. 一級結構分析胺基酸標示 網站: Expasy 工具: Colorseq MGKIGIFFGTDSGNAEAIAEKISKAIGNAEVIDVAKASKDQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDGRISKWVEQIKGSFA MGKIGIFFGTDSGNAEAIAEKISKAIGNAEVIDVAKASKDQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDGRISKWVEQIKGSFA MGKIGIFFGTDSGNAEAIAEKISKAIGNAEVIDVAKASKDQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDGRISKWVEQIKGSFA MGKIGIFFGTDSGNAEAIAEKISKAIGNAEVIDVAKASKDQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDGRISKWVEQIKGSFA AGILPVFYWDENQRHSTKCM Positive KHR Aromatic FWY Hydrophobic ALIVMW

  17. 三級結構預測 網站: Expasy 工具: 3D-PSSM THE PAIRWISE RMSD BETWEEN THE STRUCTURES IS : 0.131181 1 : /pdb1czlA_0.tmp TEMPLATE 2 : /model_1.pdb SELECTED

  18. 序列結構蛋白質結構預測流程 待測蛋白質序列 http://www.bmm.icnet.uk/people/rob/CCP11BBS/flowchart2.html 蛋白質序列比對 資料庫蒐尋 折疊辨認 是否有 PDB資料 No 預測二級結構 是否有 折疊資料 yes 二級結構比對 yes No 比對模擬 序列-結構比對 預測三級結構 3D 結構模型

  19. 蛋白質結構預測之方法 • Homology modeling • Recognition fold • Ab-inition

  20. 生物資訊在生物技術之應用 • 電子鼻感測原件分子識別材料 Chemistry (The chinese Chem. Soc., Taipei) June 2001 Vol. 59 No. 2 pp.235-243.

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